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Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis)

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Relation http://oar.icrisat.org/11745/
https://doi.org/10.1093/gigascience/giab013
doi:10.1093/gigascience/giab013
 
Title Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis)
 
Creator Wang, X
Chen, S
Ma, X
Yssel, A E J
Chaluvadi, S R
Johnson, M S
Gangashetty, P
Hamidou, F
Sanogo, M D
Zwaenepoel, A
Wallace, J
de Peer, Y
Bennetzen, J L
Van Deynze, A
 
Subject Cereals
Millets
Genetics and Genomics
 
Description Digitaria exilis, white fonio, is a minor but vital crop of West Africa that is valued for its resilience in hot, dry,
and low-fertility environments and for the exceptional quality of its grain for human nutrition. Its success is hindered,
however, by a low degree of plant breeding and improvement. Findings: We sequenced the fonio genome with long-read
SMRT-cell technology, yielding a ∼761 Mb assembly in 3,329 contigs (N50, 1.73 Mb; L50, 126). The assembly approaches a
high level of completion, with a BUSCO score of >99%. The fonio genome was found to be a tetraploid, with most of the
genome retained as homoeologous duplications that differ overall by ∼4.3%, neglecting indels. The 2 genomes within fonio were found to have begun their independent divergence ∼3.1 million years ago. The repeat content (>49%) is fairly standard
for a grass genome of this size, but the ratio of Gypsy to Copia long terminal repeat retrotransposons (∼6.7) was found to be
exceptionally high. Several genes related to future improvement of the crop were identified including shattering, plant
height, and grain size. Analysis of fonio population genetics, primarily in Mali, indicated that the crop has extensive genetic
diversity that is largely partitioned across a north-south gradient coinciding with the Sahel and Sudan grassland domains.
Conclusions: We provide a high-quality assembly, annotation, and diversity analysis for a vital African crop. The availability
of this information should empower future research into further domestication and improvement of fonio.
 
Publisher Oxford University Press
 
Date 2021-03
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Identifier http://oar.icrisat.org/11745/1/Wangetal.2021Genomesequence.pdf
Wang, X and Chen, S and Ma, X and Yssel, A E J and Chaluvadi, S R and Johnson, M S and Gangashetty, P and Hamidou, F and Sanogo, M D and Zwaenepoel, A and Wallace, J and de Peer, Y and Bennetzen, J L and Van Deynze, A (2021) Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis). GigaScience (TSI), 10 (3). pp. 1-11. ISSN 2047-217X